DAISIE

DAISIE simulates and computes the likelihood of a dynamical model of island biota assembly through speciation, immigration, and extinction.

Key Features:

• Flexible rate modeling: Allows for flexible modeling of colonization, speciation, and extinction rates.
• Alternative likelihood computation: Offers an alternative computational approach for the model's likelihood based on the pruning algorithm used for SSE (State-dependent Speciation and Extinction) models, which traces lineage history backward in time from the present day to the root of the tree.
• Computational efficiency: Provides greater computational efficiency compared to the original DAISIE likelihood computation.
• State-dependent dynamics framework: Provides a flexible framework for incorporating state-dependent dynamics in colonization, speciation, and extinction processes.
• Diversity-independent assumption: Computes likelihood under the assumption of diversity-independent colonization and diversification.

Scientific Applications:

• Island biodiversity research: Estimates from phylogenetic data the contribution of colonization, speciation and extinction to island community assembly.
• Island community assembly dynamics: Studies how assembly processes vary over time, across lineages, and across different islands.
• Colonization and diversification inference: Infers colonization and diversification dynamics on islands, including under diversity-dependence.
• Model validation: Reproduces and independently evaluates DAISIE predictions for diversity-independent colonization and diversification.

Methodology:

The alternative likelihood computation uses the pruning algorithm that traces lineage history backward in time from the present day to the root of the tree, as previously used for computing the likelihood of SSE (State-dependent Speciation and Extinction) models.